; matrix-scan -v 1 -quick -matrix_format transfac -m $RSAT/public_html/tmp/www-data/2026/08/17/matrix-scan_2026-08-17.163949_WpJW8Q.matrix -pseudo 1 -decimals 1 -2str -origin end -bgfile $RSAT/public_html/data/genomes/Arabidopsis_thaliana.TAIR10.60/oligo-frequencies/2nt_upstream-noorf_Arabidopsis_thaliana.TAIR10.60-ovlp-1str.freq -bg_pseudo 0.01 -return limits -return pval -uth pval 0.001 -i $RSAT/public_html/tmp/www-data/2026/08/17/tmp_sequence_2026-08-17.163949_botrIf.fasta -seq_format fasta -n score ; Quick counting mode ; Input files ; input $RSAT/public_html/tmp/www-data/2026/08/17/tmp_sequence_2026-08-17.163949_botrIf.fasta ; bg $RSAT/public_html/data/genomes/Arabidopsis_thaliana.TAIR10.60/oligo-frequencies/2nt_upstream-noorf_Arabidopsis_thaliana.TAIR10.60-ovlp-1str.freq ; Matrix files ; matrix 1 $RSAT/public_html/tmp/www-data/2026/08/17/matrix-scan_2026-08-17.163949_WpJW8Q.matrix ; Sequence format fasta ; Pseudo counts 1 ; Background model ; Method file ; Markov order 1 ; Strand sensitive ; Background pseudo-frequency 0.01 ; Residue probabilities ; a 0.34589 ; c 0.15671 ; g 0.15366 ; t 0.34374 ; Thresholds lower upper ; pval NA 0.001 ; Output columns ; 1 seq_id ; 2 ft_type ; 3 ft_name ; 4 strand ; 5 start ; 6 end ; 7 sequence ; 8 weight #seq_id ft_type ft_name strand start end sequence weight Pval ln_Pval sig B3GALT5 limit START_END D -500 -1 . 0 0 0 0 AT4G27590 limit START_END D -500 -1 . 0 0 0 0 SBH2 limit START_END D -500 -1 . 0 0 0 0 AT3G21420 limit START_END D -500 -1 . 0 0 0 0 AT4G16030 limit START_END D -500 -1 . 0 0 0 0 SNOR30 limit START_END D -500 -1 . 0 0 0 0 AT1G53640 limit START_END D -500 -1 . 0 0 0 0 PP2A15 limit START_END D -500 -1 . 0 0 0 0 GAMT1 limit START_END D -500 -1 . 0 0 0 0 SMXL5 limit START_END D -500 -1 . 0 0 0 0 PCR8 limit START_END D -500 -1 . 0 0 0 0 AT1G04237 limit START_END D -500 -1 . 0 0 0 0 CBSCBSPB5 limit START_END D -500 -1 . 0 0 0 0 RABA6B limit START_END D -500 -1 . 0 0 0 0 HOL2 limit START_END D -500 -1 . 0 0 0 0 AT1G09043 limit START_END D -500 -1 . 0 0 0 0 AT2G41440 limit START_END D -500 -1 . 0 0 0 0 AT1G34350 limit START_END D -500 -1 . 0 0 0 0 FIGL1 limit START_END D -500 -1 . 0 0 0 0 AT2G03955 limit START_END D -500 -1 . 0 0 0 0 AT1G07100 limit START_END D -500 -1 . 0 0 0 0 ARAC4 limit START_END D -500 -1 . 0 0 0 0 ATEXO70C1 limit START_END D -500 -1 . 0 0 0 0 LECRK31 limit START_END D -500 -1 . 0 0 0 0 NLP5 limit START_END D -500 -1 . 0 0 0 0 SCPL1 limit START_END D -500 -1 . 0 0 0 0 CRK limit START_END D -500 -1 . 0 0 0 0 AT3G01985 limit START_END D -500 -1 . 0 0 0 0 AT4G27590 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -179 -172 TATCCCAC 5.1 6.7e-04 -7.308 3.174 AT4G16030 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -486 -479 TTCCACGC 5.1 6.7e-04 -7.308 3.174 AT4G16030 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -93 -86 TTTCTCGC 7.4 6.6e-05 -9.626 4.180 AT4G16030 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -82 -75 TTTCCCCC 6.7 2.5e-04 -8.294 3.602 AT4G16030 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -15 -8 TTCACCGC 5.1 6.7e-04 -7.308 3.174 SNOR30 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -223 -216 TCTCCCTC 4.9 8.0e-04 -7.131 3.097 SNOR30 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -126 -119 AACCCCGC 5.2 5.9e-04 -7.435 3.229 AT1G53640 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -73 -66 CTTCCCGT 5.4 4.2e-04 -7.775 3.377 GAMT1 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -489 -482 TTTCACGC 7.4 6.6e-05 -9.626 4.180 GAMT1 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -214 -207 ATTCCAGC 6.7 2.5e-04 -8.294 3.602 AT1G04237 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -87 -80 CTTCCCGG 5.3 5.9e-04 -7.435 3.229 CBSCBSPB5 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -177 -170 GTTCCCGC 8.4 1.5e-05 -11.107 4.824 CBSCBSPB5 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -166 -159 TATCACGC 5.6 3.5e-04 -7.958 3.456 CBSCBSPB5 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -13 -6 TTTCCCTC 6.9 1.9e-04 -8.568 3.721 AT1G09043 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -70 -63 TCTCTCGC 5.4 4.2e-04 -7.775 3.377 AT1G09043 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -32 -25 TATCCCGA 5.3 5.1e-04 -7.581 3.292 AT1G09043 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -13 -6 TTACCCGC 8.3 1.8e-05 -10.925 4.745 AT2G41440 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -369 -362 ATACACGC 5.2 6.7e-04 -7.308 3.174 AT2G41440 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -38 -31 ATACCCTC 4.7 9.5e-04 -6.959 3.022 FIGL1 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -445 -438 TATCCCGT 5.4 4.2e-04 -7.775 3.377 FIGL1 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -253 -246 TTACCCTC 5.1 7.4e-04 -7.209 3.131 AT2G03955 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -168 -161 ATTCCCGT 6.8 2.1e-04 -8.468 3.678 ATEXO70C1 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -281 -274 TTTTCCGC 7.2 1.0e-04 -9.210 4.000 ATEXO70C1 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -76 -69 CTTCCAGC 5.3 5.1e-04 -7.581 3.292 NLP5 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -419 -412 TTCGCCGC 5.4 4.2e-04 -7.775 3.377 SCPL1 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -229 -222 TTTTCCGC 7.2 1.0e-04 -9.210 4.000 AT3G01985 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -255 -248 AATCACGC 4.8 9.5e-04 -6.959 3.022 AT4G27590 site 5015_E2Fb_Athamap_20091028_ R -179 -172 TATCCCAC 5.1 6.5e-04 -7.339 3.187 AT4G16030 site 5015_E2Fb_Athamap_20091028_ D -486 -479 TTCCACGC 5.1 6.5e-04 -7.339 3.187 AT4G16030 site 5015_E2Fb_Athamap_20091028_ R -93 -86 TTTCTCGC 7.6 5.8e-05 -9.755 4.237 AT4G16030 site 5015_E2Fb_Athamap_20091028_ R -82 -75 TTTCCCCC 6.9 1.9e-04 -8.568 3.721 AT4G16030 site 5015_E2Fb_Athamap_20091028_ D -15 -8 TTCACCGC 5.1 6.5e-04 -7.339 3.187 SNOR30 site 5015_E2Fb_Athamap_20091028_ R -223 -216 TCTCCCTC 4.8 7.5e-04 -7.195 3.125 SNOR30 site 5015_E2Fb_Athamap_20091028_ D -126 -119 AACCCCGC 4.8 7.5e-04 -7.195 3.125 AT1G53640 site 5015_E2Fb_Athamap_20091028_ D -73 -66 CTTCCCGT 5.3 5.1e-04 -7.581 3.292 GAMT1 site 5015_E2Fb_Athamap_20091028_ D -489 -482 TTTCACGC 7.6 5.8e-05 -9.755 4.237 GAMT1 site 5015_E2Fb_Athamap_20091028_ D -214 -207 ATTCCAGC 6.6 2.4e-04 -8.335 3.620 AT1G04237 site 5015_E2Fb_Athamap_20091028_ R -87 -80 CTTCCCGG 5.1 5.8e-04 -7.452 3.237 CBSCBSPB5 site 5015_E2Fb_Athamap_20091028_ D -177 -170 GTTCCCGC 8.6 1.5e-05 -11.107 4.824 CBSCBSPB5 site 5015_E2Fb_Athamap_20091028_ R -166 -159 TATCACGC 5.6 3.3e-04 -8.016 3.481 CBSCBSPB5 site 5015_E2Fb_Athamap_20091028_ D -13 -6 TTTCCCTC 7.1 1.7e-04 -8.680 3.770 AT1G09043 site 5015_E2Fb_Athamap_20091028_ D -70 -63 TCTCTCGC 5.4 4.4e-04 -7.729 3.357 AT1G09043 site 5015_E2Fb_Athamap_20091028_ R -32 -25 TATCCCGA 5.3 4.4e-04 -7.729 3.357 AT1G09043 site 5015_E2Fb_Athamap_20091028_ R -13 -6 TTACCCGC 8.5 1.8e-05 -10.925 4.745 AT2G41440 site 5015_E2Fb_Athamap_20091028_ D -369 -362 ATACACGC 4.7 7.9e-04 -7.143 3.102 FIGL1 site 5015_E2Fb_Athamap_20091028_ D -445 -438 TATCCCGT 5.4 4.4e-04 -7.729 3.357 FIGL1 site 5015_E2Fb_Athamap_20091028_ R -253 -246 TTACCCTC 5.0 6.5e-04 -7.339 3.187 AT2G03955 site 5015_E2Fb_Athamap_20091028_ D -168 -161 ATTCCCGT 6.6 2.4e-04 -8.335 3.620 ATEXO70C1 site 5015_E2Fb_Athamap_20091028_ R -281 -274 TTTTCCGC 7.4 9.3e-05 -9.283 4.032 ATEXO70C1 site 5015_E2Fb_Athamap_20091028_ D -76 -69 CTTCCAGC 5.2 5.1e-04 -7.581 3.292 NLP5 site 5015_E2Fb_Athamap_20091028_ R -419 -412 TTCGCCGC 5.4 4.4e-04 -7.729 3.357 SCPL1 site 5015_E2Fb_Athamap_20091028_ R -229 -222 TTTTCCGC 7.4 9.3e-05 -9.283 4.032 AT4G27590 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ R -183 -173 ATCCCACCAAA 7.1 1.1e-04 -9.115 3.959 SBH2 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -344 -334 TGCCCTCGCAA 5.6 3.6e-04 -7.929 3.444 SBH2 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -251 -241 TACGCGATCTT 5.2 5.0e-04 -7.601 3.301 AT3G21420 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ R -247 -237 TTCACTCCAAT 4.9 6.5e-04 -7.339 3.187 AT4G16030 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ R -97 -87 TTCTCGCGGTA 6.1 2.7e-04 -8.217 3.569 AT4G16030 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ R -86 -76 TTCCCCCTAGT 4.4 9.8e-04 -6.928 3.009 SNOR30 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ R -359 -349 CTCCGGCGATT 5.0 6.5e-04 -7.339 3.187 SNOR30 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -125 -115 ACCCCGCTGAT 4.5 9.1e-04 -7.002 3.041 AT1G53640 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -72 -62 TTCCCGTAATT 5.2 5.4e-04 -7.524 3.268 GAMT1 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -488 -478 TTCACGCTATA 7.8 5.3e-05 -9.845 4.276 GAMT1 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -213 -203 TTCCAGCTAGA 5.1 5.4e-04 -7.524 3.268 GAMT1 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ R -192 -182 TTACCACCAAA 5.0 6.0e-04 -7.419 3.222 AT1G04237 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -149 -139 GACCAGCCATA 5.0 6.5e-04 -7.339 3.187 CBSCBSPB5 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -374 -364 TTCACGTCATT 4.9 6.5e-04 -7.339 3.187 CBSCBSPB5 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -176 -166 TTCCCGCGTAG 7.3 9.0e-05 -9.316 4.046 CBSCBSPB5 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -12 -2 TTCCCTCTCCT 4.7 8.3e-04 -7.094 3.081 AT1G09043 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -416 -406 AACCCACCATT 5.3 4.6e-04 -7.684 3.337 AT1G09043 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ R -305 -295 TACCTACCCAA 4.6 8.3e-04 -7.094 3.081 AT1G09043 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ R -17 -7 TACCCGCTATT 9.5 8.0e-06 -11.736 5.097 AT2G41440 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -368 -358 TACACGCAAAA 5.0 6.0e-04 -7.419 3.222 AT2G41440 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -101 -91 AACGCTCCAAA 5.1 5.4e-04 -7.524 3.268 AT2G41440 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ R -81 -71 TTCTAGCCAAA 5.5 3.9e-04 -7.849 3.409 FIGL1 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ R -329 -319 AACCCACGATT 4.7 7.7e-04 -7.169 3.114 FIGL1 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ R -81 -71 ATCGGGCCCAG 4.5 9.8e-04 -6.928 3.009 FIGL1 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -47 -37 TACACGCCGTT 5.5 3.9e-04 -7.849 3.409 AT2G03955 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -402 -392 ACCCAGCCAAA 4.7 7.7e-04 -7.169 3.114 AT2G03955 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -227 -217 TACCCGAAAAA 4.5 9.1e-04 -7.002 3.041 ATEXO70C1 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ R -285 -275 TTTCCGCAATT 4.9 6.5e-04 -7.339 3.187 ATEXO70C1 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -75 -65 TTCCAGCCCTG 6.2 2.3e-04 -8.377 3.638 SCPL1 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ R -262 -252 TTTCCACCAAA 4.6 8.3e-04 -7.094 3.081 SCPL1 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ R -233 -223 TTTCCGCCAAA 8.4 2.7e-05 -10.520 4.569 CRK site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ R -185 -175 ATCCTGCCAAC 5.2 5.0e-04 -7.601 3.301 AT3G01985 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ R -259 -249 ATCACGCCCAT 8.1 3.9e-05 -10.152 4.409 ; ; Matrices ; matrix name ncol nrow pseudo Wmin Wmax Wrange ; 1 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ 8 4 0 -11.100 10.500 21.600 a:0.346 c:0.157 g:0.154 t:0.344 ; 2 5015_E2Fb_Athamap_20091028_ 8 4 0 -12.900 10.900 23.800 a:0.346 c:0.157 g:0.154 t:0.344 ; 3 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ 11 4 0 -19.800 12.800 32.600 a:0.346 c:0.157 g:0.154 t:0.344 ; Number of sequences scanned 28 ; Sum of sequence lengths 14000 ; N residues 0 ; Matches per matrix ; matrix name matches scored ; 1 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ 27 0 ; 2 5015_E2Fb_Athamap_20091028_ 25 0 ; 3 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ 33 0 ; TOTAL 85 0 ; Host name rsat ; Job started 2026-08-17.163949 ; Job done 2026-08-17.163951 ; Seconds 0.49 ; user 0.49 ; system 0.03 ; cuser 0.81 ; csystem 0.08